Fix input sampling validation and SIPNET IC handling

.github/workflows/book.yml

@@ -29,6 +29,10 @@ jobs:
         Rscript \
           -e 'repos <- c(getOption("repos"), sub(r"(\d{4}-\d{2}-\d{2})", "latest", getOption("repos")))' \
           -e 'remotes::install_version("bookdown", ">= 0.31", dependencies = TRUE, upgrade = FALSE, repos = repos)'
+    # generate package documentation
+    - name: Generate Package Documentation
+      working-directory: ./ 
+      run: make pkgdocs
     # copy files
     - name: copy extfiles
       run: |

docker/base/Dockerfile

@@ -3,6 +3,9 @@ ARG IMAGE_VERSION="latest"
 ARG PARENT_IMAGE="pecan/depends"
 FROM ${PARENT_IMAGE}:${IMAGE_VERSION}
 
+# Install R package for pkgdown
+RUN R -e "install.packages(c('pkgdown', 'remotes'))"
+
 # ----------------------------------------------------------------------
 # PEcAn version information
 # ----------------------------------------------------------------------

docker/depends/pecan_package_dependencies.csv

@@ -471,6 +471,7 @@
 "reticulate","*","modules/data.atmosphere","Suggests",FALSE
 "reticulate","*","modules/data.land","Suggests",FALSE
 "reticulate","*","modules/data.remote","Imports",FALSE
+"rhdf5","*","modules/data.remote","Suggests",FALSE
 "rjags","*","base/utils","Suggests",FALSE
 "rjags","*","modules/assim.batch","Imports",FALSE
 "rjags","*","modules/data.land","Imports",FALSE

models/sipnet/R/write.configs.SIPNET.R

@@ -602,8 +602,8 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
 
   else if (length(settings$run$inputs$poolinitcond$path)>0) {
     ICs_num <- length(settings$run$inputs$poolinitcond$path)
-    IC.path <- settings$run$inputs$poolinitcond$path[[sample(1:ICs_num, 1)]]
-
+    IC.path <- settings$run$inputs$poolinitcond$path[[1]] 
+    
     IC.pools <- PEcAn.data.land::prepare_pools(IC.path, constants = list(sla = SLA))
 
     if(!is.null(IC.pools)){

modules/data.remote/DESCRIPTION

@@ -44,6 +44,7 @@ Suggests:
     lubridate,
     raster,
     reshape,
+    rhdf5,
     sf,
     testthat (>= 1.0.2),
     tibble,

modules/uncertainty/R/ensemble.R

@@ -214,6 +214,29 @@ get.ensemble.samples <- function(ensemble.size, pft.samples, env.samples,
 write.ensemble.configs <- function(defaults, ensemble.samples, settings, model, 
                                    clean = FALSE, write.to.db = TRUE, restart = NULL, samples = NULL, rename = FALSE) {
 
+
+  # Check if there are NO inputs
+
+for (input_tag in names(settings$run$inputs)) {
+  input <- settings$run$inputs[[input_tag]]
+  input_paths <- input$path
+
+  # Check for required paths
+  if (is.null(input_paths) || length(input_paths) == 0) {
+     PEcAn.logger::logger.error("Input", sQuote(input_tag), "has no paths specified")
+  }
+
+  # Check for unsampled multi-path inputs
+  if (length(input_paths) > 1 && 
+     !(input_tag %in% names(settings$ensemble$samplingspace))) {
+    PEcAn.logger::logger.error(
+      "Input", sQuote(input_tag), "has", length(input_paths), "paths but no sampling method.",
+      "Add <samplingspace> for this input in pecan.xml")
+  }
+}
+
+
+
   con <- NULL
   my.write.config <- paste("write.config.", model, sep = "")
   my.write_restart <- paste0("write_restart.", model)
@@ -414,7 +437,26 @@ write.ensemble.configs <- function(defaults, ensemble.samples, settings, model,
           "rundir      : ", file.path(settings$host$rundir, run.id), "\n",
           "outdir      : ", file.path(settings$host$outdir, run.id), "\n",
           file = file.path(settings$rundir, run.id, "README.txt"))
+
+
 
+    #changing the structure of input tag to what the models are expecting
+    for (input_i in seq_along(settings$run$inputs)) {
+            input_tag <- names(settings$run$inputs)[[input_i]]
+            input <- settings$run$inputs[[input_tag]]
+
+
+     if (!input_tag %in% names(samples)) {
+        # Use first path (already validated as single path)
+        settings$run$inputs[[input_tag]]$path <- input$path[1]  } 
+        else {
+           # Use sampled path
+          settings$run$inputs[[input_tag]]$path <- samples[[input_tag]][["samples"]][[i]]
+  }
+
+}
+
+
 
       do.call(my.write.config, args = list( defaults = defaults, 
                                             trait.values = lapply(samples$parameters$samples, function(x, n) { x[n, , drop=FALSE] }, n=i), # this is the params
@@ -540,3 +582,4 @@ input.ens.gen <- function(settings, input, method = "sampling", parent_ids = NUL
 
   return(samples)
 }
+

modules/uncertainty/tests/testthat/test_ensemble.R

@@ -0,0 +1,137 @@
+library(testthat)
+library(mockery)
+
+# Source the ensemble config function
+
+context("input validation for write.ensemble.configs")
+
+# Mock a model write.configs function to avoid model-specific errors
+write.configs.SIPNET <- function(...) TRUE
+
+# Helper: make input with correct structure
+make_input_sets <- function(paths) {
+  lapply(paths, function(p) list(path = p))
+}
+
+# Helper: make ensemble.samples with the correct structure
+make_samples <- function(samples) {
+  lapply(paths, function(p) list(path = p))
+}
+
+# 1. One input, no samples → should pass
+test_that("1 input, no samples: passes", {
+  settings <- list(run = list(inputs = list(input = list(path = "IC1"))))
+  ensemble.samples <- NULL
+  defaults <- list()
+
+  expect_silent(write.ensemble.configs(
+    defaults = defaults,
+    ensemble.samples = ensemble.samples,
+    settings = settings,
+    model = "SIPNET",
+    write.to.db = FALSE
+  ))
+})
+
+
+
+test_that("no input error", {
+  settings <- list(run = list(inputs = list(input = NULL)))
+  ensemble.samples <- NULL
+  defaults <- list()
+
+  # Capture logger message
+  expect_silent(write.ensemble.configs(
+    defaults = defaults,
+    ensemble.samples = ensemble.samples,
+    settings = settings,
+    model = "SIPNET",
+    write.to.db = FALSE
+  ))
+})
+
+
+
+
+
+
+
+
+test_that("multiple inputs and multiple samples", {
+  # Mock the SIPNET config writer
+  mockery::stub(write.ensemble.configs, "write.config.SIPNET", function(...) TRUE)
+
+  # Create temp directories
+  temp_rundir <- tempfile()
+  temp_modeloutdir <- tempfile()
+  dir.create(temp_rundir)
+  dir.create(temp_modeloutdir)
+  on.exit({
+    unlink(temp_rundir, recursive = TRUE)
+    unlink(temp_modeloutdir, recursive = TRUE)
+  }, add = TRUE)
+
+  # Complete settings
+  settings <- list(
+    run = list(
+      inputs = list(input = list(path = "IC1")),
+      site = list(id = 1, name = "Test Site"),
+      start.date = "2000-01-01",
+      end.date = "2000-12-31",
+      outdir = temp_modeloutdir
+    ),
+    ensemble = list(size = 5),
+    database = NULL,
+    rundir = temp_rundir,
+    modeloutdir = temp_modeloutdir,
+    host = list(
+      rundir = temp_rundir,
+      outdir = temp_modeloutdir
+    ),
+    model = list(id = "SIPNET", type = "SIPNET"),
+    pfts = list(
+      list(name = "temperate", 
+           constants = list(1),
+           posteriorid = 1)
+    )
+  )
+
+  # Sample parameters
+  ensemble.samples <- list(
+    temperate = data.frame(
+      SLA = c(15.2, 16.8, 14.7, 18.1, 17.5),
+      Vm0 = c(45.0, 50.3, 47.8, 49.1, 51.0)
+    )
+  )
+
+  # Default PFT settings
+  defaults <- list(
+    list(
+      name = "temperate",
+      constants = list(1),
+      posteriorid = 1
+    )
+  )
+
+  # Run test - should create directories and configs
+  result <- expect_silent(
+    write.ensemble.configs(
+      defaults = defaults,
+      ensemble.samples = ensemble.samples,
+      settings = settings,
+      model = "SIPNET",
+      write.to.db = FALSE
+    )
+  )
+
+  # Verify outputs
+  expect_type(result, "list")
+  expect_named(result, c("runs", "ensemble.id", "samples"))
+  expect_equal(nrow(result$runs), settings$ensemble$size)
+})
+
+
+
+
+
+